Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:45:24.212 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:45:24 GMT 2026] MarkDuplicates --INPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:45:24 GMT 2026] Executing as ?@nf-aae263b4df523d6c6002d9183f8eed18-eb140-qqlwv on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:45:24 MarkDuplicates Start of doWork freeMemory: 105828416; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:45:24 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:45:24 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:45:30 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:8,358,604
INFO 2026-06-08 07:45:30 MarkDuplicates Tracking 1693 as yet unmatched pairs. 49 records in RAM.
INFO 2026-06-08 07:45:33 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:16,953,304
INFO 2026-06-08 07:45:33 MarkDuplicates Tracking 3728 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:45:36 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:24,661,325
INFO 2026-06-08 07:45:36 MarkDuplicates Tracking 5633 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 07:45:39 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:32,204,578
INFO 2026-06-08 07:45:39 MarkDuplicates Tracking 7424 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:45:42 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:40,314,204
INFO 2026-06-08 07:45:42 MarkDuplicates Tracking 8857 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 07:45:44 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:55,071,877
INFO 2026-06-08 07:45:44 MarkDuplicates Tracking 10567 as yet unmatched pairs. 81 records in RAM.
INFO 2026-06-08 07:45:48 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr1:109,262,915
INFO 2026-06-08 07:45:48 MarkDuplicates Tracking 12057 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 07:45:50 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:143,599,120
INFO 2026-06-08 07:45:50 MarkDuplicates Tracking 13873 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 07:45:53 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:149,935,299
INFO 2026-06-08 07:45:53 MarkDuplicates Tracking 14634 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:45:56 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:154,489,268
INFO 2026-06-08 07:45:56 MarkDuplicates Tracking 16674 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:46:00 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: chr1:156,138,686
INFO 2026-06-08 07:46:00 MarkDuplicates Tracking 18763 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 07:46:03 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:171,557,636
INFO 2026-06-08 07:46:03 MarkDuplicates Tracking 20580 as yet unmatched pairs. 112 records in RAM.
INFO 2026-06-08 07:46:05 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:202,746,142
INFO 2026-06-08 07:46:05 MarkDuplicates Tracking 22253 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:46:08 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:225,828,834
INFO 2026-06-08 07:46:08 MarkDuplicates Tracking 24033 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:46:11 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr1:248,850,288
INFO 2026-06-08 07:46:11 MarkDuplicates Tracking 25756 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:46:15 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr2:29,193,418
INFO 2026-06-08 07:46:15 MarkDuplicates Tracking 27743 as yet unmatched pairs. 27449 records in RAM.
INFO 2026-06-08 07:46:18 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-06-08 07:46:18 MarkDuplicates Tracking 258366 as yet unmatched pairs. 16473 records in RAM.
INFO 2026-06-08 07:46:22 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr2:55,049,873
INFO 2026-06-08 07:46:22 MarkDuplicates Tracking 275417 as yet unmatched pairs. 14206 records in RAM.
INFO 2026-06-08 07:46:25 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr2:85,361,743
INFO 2026-06-08 07:46:25 MarkDuplicates Tracking 273529 as yet unmatched pairs. 12309 records in RAM.
INFO 2026-06-08 07:46:28 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr2:106,073,968
INFO 2026-06-08 07:46:28 MarkDuplicates Tracking 272115 as yet unmatched pairs. 10885 records in RAM.
INFO 2026-06-08 07:46:30 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr2:130,657,166
INFO 2026-06-08 07:46:30 MarkDuplicates Tracking 271026 as yet unmatched pairs. 9785 records in RAM.
INFO 2026-06-08 07:46:33 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr2:178,537,855
INFO 2026-06-08 07:46:33 MarkDuplicates Tracking 269292 as yet unmatched pairs. 8044 records in RAM.
INFO 2026-06-08 07:46:34 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:189,009,105
INFO 2026-06-08 07:46:34 MarkDuplicates Tracking 267647 as yet unmatched pairs. 6399 records in RAM.
INFO 2026-06-08 07:46:36 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr2:215,386,766
INFO 2026-06-08 07:46:36 MarkDuplicates Tracking 265281 as yet unmatched pairs. 4025 records in RAM.
INFO 2026-06-08 07:46:38 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr2:225,817,142
INFO 2026-06-08 07:46:38 MarkDuplicates Tracking 263628 as yet unmatched pairs. 2311 records in RAM.
INFO 2026-06-08 07:46:40 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr2:240,014,816
INFO 2026-06-08 07:46:40 MarkDuplicates Tracking 261929 as yet unmatched pairs. 607 records in RAM.
INFO 2026-06-08 07:46:43 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr3:15,074,272
INFO 2026-06-08 07:46:43 MarkDuplicates Tracking 260203 as yet unmatched pairs. 13147 records in RAM.
INFO 2026-06-08 07:46:47 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 4s. Last read position: chr3:46,995,966
INFO 2026-06-08 07:46:47 MarkDuplicates Tracking 258576 as yet unmatched pairs. 11508 records in RAM.
INFO 2026-06-08 07:46:49 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr3:49,962,668
INFO 2026-06-08 07:46:49 MarkDuplicates Tracking 256195 as yet unmatched pairs. 9126 records in RAM.
INFO 2026-06-08 07:46:52 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr3:58,170,690
INFO 2026-06-08 07:46:52 MarkDuplicates Tracking 254284 as yet unmatched pairs. 7213 records in RAM.
INFO 2026-06-08 07:46:55 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr3:114,351,087
INFO 2026-06-08 07:46:55 MarkDuplicates Tracking 252476 as yet unmatched pairs. 5395 records in RAM.
INFO 2026-06-08 07:46:58 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr3:138,010,188
INFO 2026-06-08 07:46:58 MarkDuplicates Tracking 250522 as yet unmatched pairs. 3419 records in RAM.
INFO 2026-06-08 07:47:01 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr3:184,458,786
INFO 2026-06-08 07:47:01 MarkDuplicates Tracking 248564 as yet unmatched pairs. 1450 records in RAM.
INFO 2026-06-08 07:47:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr4:1,212,219
INFO 2026-06-08 07:47:03 MarkDuplicates Tracking 246745 as yet unmatched pairs. 5482 records in RAM.
INFO 2026-06-08 07:47:06 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr4:39,321,287
INFO 2026-06-08 07:47:06 MarkDuplicates Tracking 245304 as yet unmatched pairs. 4030 records in RAM.
INFO 2026-06-08 07:47:09 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr4:88,523,499
INFO 2026-06-08 07:47:09 MarkDuplicates Tracking 243579 as yet unmatched pairs. 2271 records in RAM.
INFO 2026-06-08 07:47:11 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr4:150,817,217
INFO 2026-06-08 07:47:11 MarkDuplicates Tracking 242251 as yet unmatched pairs. 915 records in RAM.
INFO 2026-06-08 07:47:14 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr5:14,316,647
INFO 2026-06-08 07:47:14 MarkDuplicates Tracking 240805 as yet unmatched pairs. 10689 records in RAM.
INFO 2026-06-08 07:47:17 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr5:67,163,379
INFO 2026-06-08 07:47:17 MarkDuplicates Tracking 238709 as yet unmatched pairs. 8577 records in RAM.
INFO 2026-06-08 07:47:20 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr5:114,362,648
INFO 2026-06-08 07:47:20 MarkDuplicates Tracking 237185 as yet unmatched pairs. 7039 records in RAM.
INFO 2026-06-08 07:47:23 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr5:139,561,737
INFO 2026-06-08 07:47:23 MarkDuplicates Tracking 235618 as yet unmatched pairs. 5469 records in RAM.
INFO 2026-06-08 07:47:25 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: chr5:150,123,180
INFO 2026-06-08 07:47:25 MarkDuplicates Tracking 234443 as yet unmatched pairs. 4073 records in RAM.
INFO 2026-06-08 07:47:29 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr5:168,616,430
INFO 2026-06-08 07:47:29 MarkDuplicates Tracking 232961 as yet unmatched pairs. 2589 records in RAM.
INFO 2026-06-08 07:47:31 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr5:179,822,965
INFO 2026-06-08 07:47:31 MarkDuplicates Tracking 231354 as yet unmatched pairs. 975 records in RAM.
INFO 2026-06-08 07:47:33 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr6:17,735,968
INFO 2026-06-08 07:47:33 MarkDuplicates Tracking 229355 as yet unmatched pairs. 11967 records in RAM.
INFO 2026-06-08 07:47:36 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr6:31,632,916
INFO 2026-06-08 07:47:36 MarkDuplicates Tracking 228071 as yet unmatched pairs. 10679 records in RAM.
INFO 2026-06-08 07:47:39 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr6:32,195,892
INFO 2026-06-08 07:47:39 MarkDuplicates Tracking 226225 as yet unmatched pairs. 8832 records in RAM.
INFO 2026-06-08 07:47:41 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr6:42,262,470
INFO 2026-06-08 07:47:41 MarkDuplicates Tracking 224580 as yet unmatched pairs. 7181 records in RAM.
INFO 2026-06-08 07:47:44 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr6:81,555,345
INFO 2026-06-08 07:47:44 MarkDuplicates Tracking 222430 as yet unmatched pairs. 5022 records in RAM.
INFO 2026-06-08 07:47:47 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr6:129,791,548
INFO 2026-06-08 07:47:47 MarkDuplicates Tracking 220612 as yet unmatched pairs. 3190 records in RAM.
INFO 2026-06-08 07:47:49 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr6:152,060,989
INFO 2026-06-08 07:47:49 MarkDuplicates Tracking 218724 as yet unmatched pairs. 1299 records in RAM.
INFO 2026-06-08 07:47:52 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr7:2,433,473
INFO 2026-06-08 07:47:52 MarkDuplicates Tracking 216761 as yet unmatched pairs. 13579 records in RAM.
INFO 2026-06-08 07:47:56 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 3s. Last read position: chr7:23,512,963
INFO 2026-06-08 07:47:56 MarkDuplicates Tracking 214848 as yet unmatched pairs. 11658 records in RAM.
INFO 2026-06-08 07:47:58 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr7:55,201,279
INFO 2026-06-08 07:47:58 MarkDuplicates Tracking 213194 as yet unmatched pairs. 9997 records in RAM.
INFO 2026-06-08 07:48:00 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr7:75,340,724
INFO 2026-06-08 07:48:00 MarkDuplicates Tracking 212057 as yet unmatched pairs. 8849 records in RAM.
INFO 2026-06-08 07:48:03 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr7:94,408,212
INFO 2026-06-08 07:48:03 MarkDuplicates Tracking 210572 as yet unmatched pairs. 7361 records in RAM.
INFO 2026-06-08 07:48:06 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr7:100,430,873
INFO 2026-06-08 07:48:06 MarkDuplicates Tracking 208519 as yet unmatched pairs. 5302 records in RAM.
INFO 2026-06-08 07:48:08 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr7:107,261,316
INFO 2026-06-08 07:48:08 MarkDuplicates Tracking 206780 as yet unmatched pairs. 3556 records in RAM.
INFO 2026-06-08 07:48:11 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr7:139,583,979
INFO 2026-06-08 07:48:11 MarkDuplicates Tracking 205186 as yet unmatched pairs. 1939 records in RAM.
INFO 2026-06-08 07:48:12 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr7:151,142,603
INFO 2026-06-08 07:48:12 MarkDuplicates Tracking 203864 as yet unmatched pairs. 613 records in RAM.
INFO 2026-06-08 07:48:15 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr8:22,556,875
INFO 2026-06-08 07:48:15 MarkDuplicates Tracking 202237 as yet unmatched pairs. 9112 records in RAM.
INFO 2026-06-08 07:48:19 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 3s. Last read position: chr8:38,429,886
INFO 2026-06-08 07:48:19 MarkDuplicates Tracking 200405 as yet unmatched pairs. 7273 records in RAM.
INFO 2026-06-08 07:48:22 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 3s. Last read position: chr8:93,719,056
INFO 2026-06-08 07:48:22 MarkDuplicates Tracking 198290 as yet unmatched pairs. 5143 records in RAM.
INFO 2026-06-08 07:48:25 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr8:140,152,291
INFO 2026-06-08 07:48:25 MarkDuplicates Tracking 196471 as yet unmatched pairs. 3315 records in RAM.
INFO 2026-06-08 07:48:28 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr8:143,924,181
INFO 2026-06-08 07:48:28 MarkDuplicates Tracking 194498 as yet unmatched pairs. 1306 records in RAM.
INFO 2026-06-08 07:48:30 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr9:14,307,087
INFO 2026-06-08 07:48:30 MarkDuplicates Tracking 193002 as yet unmatched pairs. 10836 records in RAM.
INFO 2026-06-08 07:48:33 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr9:66,920,522
INFO 2026-06-08 07:48:33 MarkDuplicates Tracking 191259 as yet unmatched pairs. 8956 records in RAM.
INFO 2026-06-08 07:48:36 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr9:99,062,260
INFO 2026-06-08 07:48:36 MarkDuplicates Tracking 189340 as yet unmatched pairs. 7029 records in RAM.
INFO 2026-06-08 07:48:38 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr9:122,204,686
INFO 2026-06-08 07:48:38 MarkDuplicates Tracking 187753 as yet unmatched pairs. 5441 records in RAM.
INFO 2026-06-08 07:48:41 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr9:130,878,444
INFO 2026-06-08 07:48:41 MarkDuplicates Tracking 185799 as yet unmatched pairs. 3481 records in RAM.
INFO 2026-06-08 07:48:44 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 3s. Last read position: chr9:136,545,731
INFO 2026-06-08 07:48:44 MarkDuplicates Tracking 183304 as yet unmatched pairs. 977 records in RAM.
INFO 2026-06-08 07:48:47 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr10:13,610,098
INFO 2026-06-08 07:48:47 MarkDuplicates Tracking 181215 as yet unmatched pairs. 8420 records in RAM.
INFO 2026-06-08 07:48:49 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr10:37,176,206
INFO 2026-06-08 07:48:49 MarkDuplicates Tracking 179846 as yet unmatched pairs. 7042 records in RAM.
INFO 2026-06-08 07:48:52 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 3s. Last read position: chr10:59,792,929
INFO 2026-06-08 07:48:52 MarkDuplicates Tracking 178201 as yet unmatched pairs. 5389 records in RAM.
INFO 2026-06-08 07:48:55 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr10:80,157,688
INFO 2026-06-08 07:48:55 MarkDuplicates Tracking 176689 as yet unmatched pairs. 3873 records in RAM.
INFO 2026-06-08 07:48:58 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr10:102,139,555
INFO 2026-06-08 07:48:58 MarkDuplicates Tracking 174705 as yet unmatched pairs. 1882 records in RAM.
INFO 2026-06-08 07:49:00 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr10:128,069,721
INFO 2026-06-08 07:49:00 MarkDuplicates Tracking 173168 as yet unmatched pairs. 296 records in RAM.
INFO 2026-06-08 07:49:03 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr11:1,757,323
INFO 2026-06-08 07:49:03 MarkDuplicates Tracking 171146 as yet unmatched pairs. 15524 records in RAM.
INFO 2026-06-08 07:49:06 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 3s. Last read position: chr11:17,288,881
INFO 2026-06-08 07:49:06 MarkDuplicates Tracking 169323 as yet unmatched pairs. 13692 records in RAM.
INFO 2026-06-08 07:49:09 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr11:57,313,676
INFO 2026-06-08 07:49:09 MarkDuplicates Tracking 167480 as yet unmatched pairs. 11838 records in RAM.
INFO 2026-06-08 07:49:12 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr11:62,529,844
INFO 2026-06-08 07:49:12 MarkDuplicates Tracking 165723 as yet unmatched pairs. 10059 records in RAM.
INFO 2026-06-08 07:49:15 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 3s. Last read position: chr11:65,424,585
INFO 2026-06-08 07:49:15 MarkDuplicates Tracking 163751 as yet unmatched pairs. 8085 records in RAM.
INFO 2026-06-08 07:49:18 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr11:67,286,378
INFO 2026-06-08 07:49:18 MarkDuplicates Tracking 162165 as yet unmatched pairs. 6499 records in RAM.
INFO 2026-06-08 07:49:20 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr11:73,309,317
INFO 2026-06-08 07:49:20 MarkDuplicates Tracking 160237 as yet unmatched pairs. 4567 records in RAM.
INFO 2026-06-08 07:49:22 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr11:103,909,785
INFO 2026-06-08 07:49:22 MarkDuplicates Tracking 158332 as yet unmatched pairs. 2644 records in RAM.
INFO 2026-06-08 07:49:25 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr11:119,744,039
INFO 2026-06-08 07:49:25 MarkDuplicates Tracking 156514 as yet unmatched pairs. 823 records in RAM.
INFO 2026-06-08 07:49:26 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr12:6,573,095
INFO 2026-06-08 07:49:26 MarkDuplicates Tracking 154924 as yet unmatched pairs. 13321 records in RAM.
INFO 2026-06-08 07:49:29 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr12:14,947,899
INFO 2026-06-08 07:49:29 MarkDuplicates Tracking 153588 as yet unmatched pairs. 11983 records in RAM.
INFO 2026-06-08 07:49:32 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 3s. Last read position: chr12:49,055,014
INFO 2026-06-08 07:49:32 MarkDuplicates Tracking 152266 as yet unmatched pairs. 10652 records in RAM.
INFO 2026-06-08 07:49:36 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 3s. Last read position: chr12:53,063,243
INFO 2026-06-08 07:49:36 MarkDuplicates Tracking 150290 as yet unmatched pairs. 8674 records in RAM.
INFO 2026-06-08 07:49:38 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr12:56,721,309
INFO 2026-06-08 07:49:38 MarkDuplicates Tracking 148676 as yet unmatched pairs. 7059 records in RAM.
INFO 2026-06-08 07:49:41 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 3s. Last read position: chr12:68,689,534
INFO 2026-06-08 07:49:41 MarkDuplicates Tracking 146798 as yet unmatched pairs. 5175 records in RAM.
INFO 2026-06-08 07:49:44 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr12:110,028,511
INFO 2026-06-08 07:49:44 MarkDuplicates Tracking 145277 as yet unmatched pairs. 3645 records in RAM.
INFO 2026-06-08 07:49:46 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr12:122,133,659
INFO 2026-06-08 07:49:46 MarkDuplicates Tracking 143398 as yet unmatched pairs. 1763 records in RAM.
INFO 2026-06-08 07:49:49 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr12:132,748,176
INFO 2026-06-08 07:49:49 MarkDuplicates Tracking 141805 as yet unmatched pairs. 164 records in RAM.
INFO 2026-06-08 07:49:51 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr13:52,029,323
INFO 2026-06-08 07:49:51 MarkDuplicates Tracking 139646 as yet unmatched pairs. 1888 records in RAM.
INFO 2026-06-08 07:49:53 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 2s. Last read position: chr14:20,380,259
INFO 2026-06-08 07:49:53 MarkDuplicates Tracking 137728 as yet unmatched pairs. 8749 records in RAM.
INFO 2026-06-08 07:49:55 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr14:34,612,995
INFO 2026-06-08 07:49:55 MarkDuplicates Tracking 135680 as yet unmatched pairs. 6697 records in RAM.
INFO 2026-06-08 07:49:58 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr14:67,691,183
INFO 2026-06-08 07:49:58 MarkDuplicates Tracking 133990 as yet unmatched pairs. 5003 records in RAM.
INFO 2026-06-08 07:50:00 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr14:75,783,330
INFO 2026-06-08 07:50:00 MarkDuplicates Tracking 132378 as yet unmatched pairs. 3389 records in RAM.
INFO 2026-06-08 07:50:03 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr14:102,903,277
INFO 2026-06-08 07:50:03 MarkDuplicates Tracking 130605 as yet unmatched pairs. 1565 records in RAM.
INFO 2026-06-08 07:50:05 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr15:25,779,094
INFO 2026-06-08 07:50:05 MarkDuplicates Tracking 128858 as yet unmatched pairs. 7984 records in RAM.
INFO 2026-06-08 07:50:08 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr15:41,835,065
INFO 2026-06-08 07:50:08 MarkDuplicates Tracking 127341 as yet unmatched pairs. 6458 records in RAM.
INFO 2026-06-08 07:50:11 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr15:61,907,327
INFO 2026-06-08 07:50:11 MarkDuplicates Tracking 125806 as yet unmatched pairs. 4922 records in RAM.
INFO 2026-06-08 07:50:13 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr15:74,043,075
INFO 2026-06-08 07:50:13 MarkDuplicates Tracking 123907 as yet unmatched pairs. 3017 records in RAM.
INFO 2026-06-08 07:50:15 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr15:85,579,623
INFO 2026-06-08 07:50:15 MarkDuplicates Tracking 122226 as yet unmatched pairs. 1323 records in RAM.
INFO 2026-06-08 07:50:17 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr16:381,792
INFO 2026-06-08 07:50:17 MarkDuplicates Tracking 120523 as yet unmatched pairs. 14092 records in RAM.
INFO 2026-06-08 07:50:20 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr16:2,757,556
INFO 2026-06-08 07:50:20 MarkDuplicates Tracking 118679 as yet unmatched pairs. 12245 records in RAM.
INFO 2026-06-08 07:50:22 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr16:4,652,016
INFO 2026-06-08 07:50:22 MarkDuplicates Tracking 117256 as yet unmatched pairs. 10818 records in RAM.
INFO 2026-06-08 07:50:25 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr16:15,363,810
INFO 2026-06-08 07:50:25 MarkDuplicates Tracking 116150 as yet unmatched pairs. 9711 records in RAM.
INFO 2026-06-08 07:50:27 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,271
INFO 2026-06-08 07:50:27 MarkDuplicates Tracking 115594 as yet unmatched pairs. 9153 records in RAM.
INFO 2026-06-08 07:50:28 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr16:21,404,973
INFO 2026-06-08 07:50:28 MarkDuplicates Tracking 115066 as yet unmatched pairs. 8625 records in RAM.
INFO 2026-06-08 07:50:30 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr16:22,527,565
INFO 2026-06-08 07:50:30 MarkDuplicates Tracking 114546 as yet unmatched pairs. 8104 records in RAM.
INFO 2026-06-08 07:50:32 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr16:27,776,901
INFO 2026-06-08 07:50:32 MarkDuplicates Tracking 113856 as yet unmatched pairs. 7414 records in RAM.
INFO 2026-06-08 07:50:34 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr16:29,485,485
INFO 2026-06-08 07:50:34 MarkDuplicates Tracking 113333 as yet unmatched pairs. 6889 records in RAM.
INFO 2026-06-08 07:50:36 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr16:30,664,846
INFO 2026-06-08 07:50:36 MarkDuplicates Tracking 112246 as yet unmatched pairs. 5796 records in RAM.
INFO 2026-06-08 07:50:38 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr16:56,502,329
INFO 2026-06-08 07:50:38 MarkDuplicates Tracking 110534 as yet unmatched pairs. 4069 records in RAM.
INFO 2026-06-08 07:50:40 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr16:70,664,597
INFO 2026-06-08 07:50:40 MarkDuplicates Tracking 108783 as yet unmatched pairs. 2309 records in RAM.
INFO 2026-06-08 07:50:42 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr16:88,624,045
INFO 2026-06-08 07:50:42 MarkDuplicates Tracking 107354 as yet unmatched pairs. 863 records in RAM.
INFO 2026-06-08 07:50:45 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr17:3,577,628
INFO 2026-06-08 07:50:45 MarkDuplicates Tracking 105362 as yet unmatched pairs. 30545 records in RAM.
INFO 2026-06-08 07:50:47 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr17:7,513,489
INFO 2026-06-08 07:50:47 MarkDuplicates Tracking 103794 as yet unmatched pairs. 28973 records in RAM.
INFO 2026-06-08 07:50:50 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr17:17,217,159
INFO 2026-06-08 07:50:50 MarkDuplicates Tracking 101876 as yet unmatched pairs. 27051 records in RAM.
INFO 2026-06-08 07:50:53 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr17:31,865,385
INFO 2026-06-08 07:50:53 MarkDuplicates Tracking 99809 as yet unmatched pairs. 24981 records in RAM.
INFO 2026-06-08 07:50:56 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr17:39,710,346
INFO 2026-06-08 07:50:56 MarkDuplicates Tracking 98226 as yet unmatched pairs. 23395 records in RAM.
INFO 2026-06-08 07:50:58 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr17:42,991,465
INFO 2026-06-08 07:50:58 MarkDuplicates Tracking 95937 as yet unmatched pairs. 21105 records in RAM.
INFO 2026-06-08 07:51:01 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 3s. Last read position: chr17:50,149,167
INFO 2026-06-08 07:51:01 MarkDuplicates Tracking 94611 as yet unmatched pairs. 19774 records in RAM.
INFO 2026-06-08 07:51:04 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,913
INFO 2026-06-08 07:51:04 MarkDuplicates Tracking 93875 as yet unmatched pairs. 19038 records in RAM.
INFO 2026-06-08 07:51:07 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,930
INFO 2026-06-08 07:51:07 MarkDuplicates Tracking 91904 as yet unmatched pairs. 17067 records in RAM.
INFO 2026-06-08 07:51:10 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,077
INFO 2026-06-08 07:51:10 MarkDuplicates Tracking 90510 as yet unmatched pairs. 15673 records in RAM.
INFO 2026-06-08 07:51:13 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr17:50,193,992
INFO 2026-06-08 07:51:13 MarkDuplicates Tracking 88737 as yet unmatched pairs. 13900 records in RAM.
INFO 2026-06-08 07:51:16 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,960
INFO 2026-06-08 07:51:16 MarkDuplicates Tracking 87352 as yet unmatched pairs. 12515 records in RAM.
INFO 2026-06-08 07:51:18 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,226
INFO 2026-06-08 07:51:18 MarkDuplicates Tracking 83688 as yet unmatched pairs. 8851 records in RAM.
INFO 2026-06-08 07:51:20 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr17:56,981,182
INFO 2026-06-08 07:51:20 MarkDuplicates Tracking 81663 as yet unmatched pairs. 6824 records in RAM.
INFO 2026-06-08 07:51:22 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr17:68,528,864
INFO 2026-06-08 07:51:22 MarkDuplicates Tracking 79706 as yet unmatched pairs. 4862 records in RAM.
INFO 2026-06-08 07:51:25 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr17:78,091,504
INFO 2026-06-08 07:51:25 MarkDuplicates Tracking 77559 as yet unmatched pairs. 2710 records in RAM.
INFO 2026-06-08 07:51:28 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 3s. Last read position: chr17:82,079,185
INFO 2026-06-08 07:51:28 MarkDuplicates Tracking 75654 as yet unmatched pairs. 803 records in RAM.
INFO 2026-06-08 07:51:31 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 3s. Last read position: chr18:36,198,901
INFO 2026-06-08 07:51:31 MarkDuplicates Tracking 73397 as yet unmatched pairs. 1805 records in RAM.
INFO 2026-06-08 07:51:34 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 3s. Last read position: chr19:860,683
INFO 2026-06-08 07:51:34 MarkDuplicates Tracking 71437 as yet unmatched pairs. 26894 records in RAM.
INFO 2026-06-08 07:51:37 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr19:3,387,249
INFO 2026-06-08 07:51:37 MarkDuplicates Tracking 68899 as yet unmatched pairs. 24353 records in RAM.
INFO 2026-06-08 07:51:40 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr19:6,415,018
INFO 2026-06-08 07:51:40 MarkDuplicates Tracking 66778 as yet unmatched pairs. 22227 records in RAM.
INFO 2026-06-08 07:51:42 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr19:10,986,954
INFO 2026-06-08 07:51:42 MarkDuplicates Tracking 65042 as yet unmatched pairs. 20486 records in RAM.
INFO 2026-06-08 07:51:45 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr19:15,161,606
INFO 2026-06-08 07:51:45 MarkDuplicates Tracking 62569 as yet unmatched pairs. 18012 records in RAM.
INFO 2026-06-08 07:51:48 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr19:17,862,161
INFO 2026-06-08 07:51:48 MarkDuplicates Tracking 60613 as yet unmatched pairs. 16041 records in RAM.
INFO 2026-06-08 07:51:51 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chr19:35,267,234
INFO 2026-06-08 07:51:51 MarkDuplicates Tracking 58294 as yet unmatched pairs. 13719 records in RAM.
INFO 2026-06-08 07:51:54 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 3s. Last read position: chr19:39,408,339
INFO 2026-06-08 07:51:54 MarkDuplicates Tracking 56077 as yet unmatched pairs. 11502 records in RAM.
INFO 2026-06-08 07:51:57 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 3s. Last read position: chr19:42,273,799
INFO 2026-06-08 07:51:57 MarkDuplicates Tracking 54202 as yet unmatched pairs. 9625 records in RAM.
INFO 2026-06-08 07:52:00 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 3s. Last read position: chr19:45,472,915
INFO 2026-06-08 07:52:00 MarkDuplicates Tracking 51963 as yet unmatched pairs. 7352 records in RAM.
INFO 2026-06-08 07:52:03 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr19:49,061,352
INFO 2026-06-08 07:52:03 MarkDuplicates Tracking 49359 as yet unmatched pairs. 4748 records in RAM.
INFO 2026-06-08 07:52:05 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr19:52,415,139
INFO 2026-06-08 07:52:05 MarkDuplicates Tracking 47211 as yet unmatched pairs. 2600 records in RAM.
INFO 2026-06-08 07:52:08 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr19:57,390,017
INFO 2026-06-08 07:52:08 MarkDuplicates Tracking 45267 as yet unmatched pairs. 652 records in RAM.
INFO 2026-06-08 07:52:11 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 3s. Last read position: chr20:17,659,071
INFO 2026-06-08 07:52:11 MarkDuplicates Tracking 43743 as yet unmatched pairs. 6149 records in RAM.
INFO 2026-06-08 07:52:14 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr20:36,786,551
INFO 2026-06-08 07:52:14 MarkDuplicates Tracking 41762 as yet unmatched pairs. 4165 records in RAM.
INFO 2026-06-08 07:52:16 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr20:53,254,486
INFO 2026-06-08 07:52:16 MarkDuplicates Tracking 39995 as yet unmatched pairs. 2397 records in RAM.
INFO 2026-06-08 07:52:19 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 2s. Last read position: chr20:64,069,360
INFO 2026-06-08 07:52:19 MarkDuplicates Tracking 37615 as yet unmatched pairs. 13 records in RAM.
INFO 2026-06-08 07:52:21 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 2s. Last read position: chr21:8,216,836
INFO 2026-06-08 07:52:21 MarkDuplicates Tracking 36661 as yet unmatched pairs. 11407 records in RAM.
INFO 2026-06-08 07:52:24 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 2s. Last read position: chr21:8,258,898
INFO 2026-06-08 07:52:24 MarkDuplicates Tracking 35733 as yet unmatched pairs. 10478 records in RAM.
INFO 2026-06-08 07:52:26 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr21:8,389,269
INFO 2026-06-08 07:52:26 MarkDuplicates Tracking 35658 as yet unmatched pairs. 10403 records in RAM.
INFO 2026-06-08 07:52:29 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr21:8,399,886
INFO 2026-06-08 07:52:29 MarkDuplicates Tracking 32751 as yet unmatched pairs. 7488 records in RAM.
INFO 2026-06-08 07:52:31 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr21:8,441,948
INFO 2026-06-08 07:52:31 MarkDuplicates Tracking 30645 as yet unmatched pairs. 5372 records in RAM.
INFO 2026-06-08 07:52:33 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,101
INFO 2026-06-08 07:52:33 MarkDuplicates Tracking 29431 as yet unmatched pairs. 4156 records in RAM.
INFO 2026-06-08 07:52:35 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 1s. Last read position: chr21:25,954,623
INFO 2026-06-08 07:52:35 MarkDuplicates Tracking 29173 as yet unmatched pairs. 3897 records in RAM.
INFO 2026-06-08 07:52:37 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr21:44,773,540
INFO 2026-06-08 07:52:37 MarkDuplicates Tracking 27683 as yet unmatched pairs. 2407 records in RAM.
INFO 2026-06-08 07:52:40 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr21:46,132,030
INFO 2026-06-08 07:52:40 MarkDuplicates Tracking 25637 as yet unmatched pairs. 360 records in RAM.
INFO 2026-06-08 07:52:42 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr22:24,269,405
INFO 2026-06-08 07:52:42 MarkDuplicates Tracking 23631 as yet unmatched pairs. 6611 records in RAM.
INFO 2026-06-08 07:52:45 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr22:36,145,516
INFO 2026-06-08 07:52:45 MarkDuplicates Tracking 22119 as yet unmatched pairs. 5098 records in RAM.
INFO 2026-06-08 07:52:49 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 3s. Last read position: chr22:40,266,160
INFO 2026-06-08 07:52:49 MarkDuplicates Tracking 19910 as yet unmatched pairs. 2887 records in RAM.
INFO 2026-06-08 07:52:52 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr22:50,437,507
INFO 2026-06-08 07:52:52 MarkDuplicates Tracking 17728 as yet unmatched pairs. 704 records in RAM.
INFO 2026-06-08 07:52:54 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chrX:32,644,979
INFO 2026-06-08 07:52:54 MarkDuplicates Tracking 16030 as yet unmatched pairs. 5290 records in RAM.
INFO 2026-06-08 07:52:57 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chrX:54,930,279
INFO 2026-06-08 07:52:57 MarkDuplicates Tracking 14206 as yet unmatched pairs. 3460 records in RAM.
INFO 2026-06-08 07:52:59 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 2s. Last read position: chrX:118,907,494
INFO 2026-06-08 07:52:59 MarkDuplicates Tracking 12661 as yet unmatched pairs. 1909 records in RAM.
INFO 2026-06-08 07:53:02 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chrX:154,368,047
INFO 2026-06-08 07:53:02 MarkDuplicates Tracking 11080 as yet unmatched pairs. 324 records in RAM.
INFO 2026-06-08 07:53:04 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,176
INFO 2026-06-08 07:53:04 MarkDuplicates Tracking 10531 as yet unmatched pairs. 2460 records in RAM.
INFO 2026-06-08 07:53:05 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,328
INFO 2026-06-08 07:53:05 MarkDuplicates Tracking 8196 as yet unmatched pairs. 122 records in RAM.
INFO 2026-06-08 07:53:07 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,127
INFO 2026-06-08 07:53:07 MarkDuplicates Tracking 8216 as yet unmatched pairs. 142 records in RAM.
INFO 2026-06-08 07:53:09 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: GL000220.1:160,284
INFO 2026-06-08 07:53:09 MarkDuplicates Tracking 8099 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 07:53:12 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: KI270733.1:129,682
INFO 2026-06-08 07:53:12 MarkDuplicates Tracking 7986 as yet unmatched pairs. 7980 records in RAM.
INFO 2026-06-08 07:53:15 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 3s. Last read position: KI270733.1:132,335
INFO 2026-06-08 07:53:15 MarkDuplicates Tracking 2513 as yet unmatched pairs. 2507 records in RAM.
INFO 2026-06-08 07:53:18 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 2s. Last read position: KI270733.1:148,214
INFO 2026-06-08 07:53:18 MarkDuplicates Tracking 367 as yet unmatched pairs. 361 records in RAM.
INFO 2026-06-08 07:53:20 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 2s. Last read position: KI270733.1:176,187
INFO 2026-06-08 07:53:20 MarkDuplicates Tracking 120 as yet unmatched pairs. 114 records in RAM.
INFO 2026-06-08 07:53:22 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 2s. Last read position: KI270733.1:178,729
INFO 2026-06-08 07:53:22 MarkDuplicates Tracking 11 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:53:22 MarkDuplicates Read 180139752 records. 0 pairs never matched.
INFO 2026-06-08 07:53:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 37519412280; totalMemory: 57042534400; maxMemory: 63585648640
INFO 2026-06-08 07:53:33 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:53:40 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:53:56 OpticalDuplicateFinder Large duplicate set. size = 1158
INFO 2026-06-08 07:53:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,883
INFO 2026-06-08 07:54:27 OpticalDuplicateFinder Large duplicate set. size = 1355
INFO 2026-06-08 07:54:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,554
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder Large duplicate set. size = 1033
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,883
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder Large duplicate set. size = 1037
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,231
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder Large duplicate set. size = 1249
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,353
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder Large duplicate set. size = 1042
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,806
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder Large duplicate set. size = 1124
INFO 2026-06-08 07:54:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,604
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1091
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,878
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1630
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,598
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1137
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,411
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1143
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,070
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1935
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,612
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1610
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,508
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder Large duplicate set. size = 1015
INFO 2026-06-08 07:54:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,401
INFO 2026-06-08 07:54:39 OpticalDuplicateFinder Large duplicate set. size = 1018
INFO 2026-06-08 07:54:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,990
INFO 2026-06-08 07:54:39 OpticalDuplicateFinder Large duplicate set. size = 1257
INFO 2026-06-08 07:54:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,889
INFO 2026-06-08 07:54:39 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:54:53 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:55:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300759736; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:55:01 MarkDuplicates Marking 133365941 records as duplicates.
INFO 2026-06-08 07:55:01 MarkDuplicates Found 3000938 optical duplicate clusters.
INFO 2026-06-08 07:55:01 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:55:26 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr1:154,489,268
INFO 2026-06-08 07:55:53 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 27s. Last read position: chr2:106,073,968
INFO 2026-06-08 07:56:19 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:18s. Time for last 10,000,000: 25s. Last read position: chr3:58,170,690
INFO 2026-06-08 07:56:46 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:45s. Time for last 10,000,000: 26s. Last read position: chr5:114,362,648
INFO 2026-06-08 07:57:11 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:10s. Time for last 10,000,000: 25s. Last read position: chr6:129,791,548
INFO 2026-06-08 07:57:36 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:35s. Time for last 10,000,000: 25s. Last read position: chr7:151,142,603
INFO 2026-06-08 07:58:01 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:00s. Time for last 10,000,000: 24s. Last read position: chr9:130,878,444
INFO 2026-06-08 07:58:27 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:26s. Time for last 10,000,000: 25s. Last read position: chr11:57,313,676
INFO 2026-06-08 07:58:52 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 25s. Last read position: chr12:53,063,243
INFO 2026-06-08 07:59:19 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 26s. Last read position: chr14:75,783,330
INFO 2026-06-08 07:59:44 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 25s. Last read position: chr16:15,363,810
INFO 2026-06-08 08:00:09 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:08s. Time for last 10,000,000: 25s. Last read position: chr17:3,577,628
INFO 2026-06-08 08:00:34 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:33s. Time for last 10,000,000: 24s. Last read position: chr17:50,193,992
INFO 2026-06-08 08:00:59 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:58s. Time for last 10,000,000: 24s. Last read position: chr19:6,415,018
INFO 2026-06-08 08:01:23 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:22s. Time for last 10,000,000: 24s. Last read position: chr19:57,390,017
INFO 2026-06-08 08:01:48 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 24s. Last read position: chr21:8,444,101
INFO 2026-06-08 08:02:14 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:07:13s. Time for last 10,000,000: 25s. Last read position: chrX:118,907,494
INFO 2026-06-08 08:02:39 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:07:38s. Time for last 10,000,000: 24s. Last read position: KI270733.1:178,729
INFO 2026-06-08 08:02:46 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:02:46 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:02:46 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:02:46 MarkDuplicates Before output close freeMemory: 5805968920; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:02:46 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:02:47 MarkDuplicates After output close freeMemory: 203904992; totalMemory: 234881024; maxMemory: 63585648640
[Mon Jun 08 08:02:47 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 17.38 minutes.
Runtime.totalMemory()=234881024
ls: *cram: No such file or directory
ls: *.crai: No such file or directory